MolNFT v1 · #124433 · protein
Crystal structure of FN3 domain (residues P368-P466) of human collagen xx
5KF4 · Collagen alpha-1(XX) chain: “Crystal structure of FN3 domain (residues P368-P466) of human collagen xx”. X-ray diffraction, 4 pockets (best druggability 0.75). MolNFT v1 #124433 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5KF4
- Type
- protein
- Length
- 391 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha-1(XX) chain
- UniProt
- Q9P218
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Collagen alpha-1(XX) chain | protein | 99 | 0% helix, 51% strand | Q9P218 |
| C | Collagen alpha-1(XX) chain | protein | 96 | 0% helix, 52% strand | Q9P218 |
| D | Collagen alpha-1(XX) chain | protein | 97 | 0% helix, 52% strand | Q9P218 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.75 | 0.78 | 99 | empty |
| 2 | 221 | 0.48 | 0.74 | 38 | empty |
| 3 | 80 | 0.31 | 0.73 | 20 | empty |
| 4 | 58 | 0.27 | 0.74 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–D · 401 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 397 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 188 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 146 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KF4 · Crystal structure of FN3 domain (Residues P368-P466) of Human collagen XX · the same entry in another collection · chain D against D, TM-score 1.00
- Q9P218 · AlphaFold monomer V2.0 prediction for collagen alpha-1(XX) chain (Q9P218) · a predicted model of the same protein · chain B against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9P218
- Elsewhere: RCSB PDB 5KF4 · PDBe 5KF4 · UniProt Q9P218
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